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cancer
•
reset
0
votes
0
replies
12k
views
Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors
Cancer
convert
Cancer
convert
12.5 years ago
Chao-Jen Wong
▴ 580
0
votes
1
reply
11k
views
heatmap.2 - change column & row locations; angle / rotate
Cancer
Cancer
written 10.4 years ago by
Cheng, Yong-Sheng
▴ 10
0
votes
4
replies
10k
views
Correlation matrix and pca on matrix with NA values
Cancer
Cancer
updated 17.0 years ago by
Aedin Culhane
▴ 510 • written 17.0 years ago by
Daniel Brewer
★ 1.9k
0
votes
6
replies
9.6k
views
Gene symbol to KEGG gene ids
Annotation
Cancer
Annotation
Cancer
updated 15.0 years ago by
Marc Carlson
★ 7.2k • written 15.0 years ago by
Daniel Brewer
★ 1.9k
4
votes
1
reply
8.5k
views
WGCNA-unable to install GO.db package
go
cancer
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
852108577
▴ 20
0
votes
1
reply
7.5k
views
Help with "Error in Summary.factor(..., na.rm = na.rm) : "max" not meaningful for factors", please?
Cancer
Cancer
updated 20.8 years ago by
Ramon Diaz
★ 1.1k • written 20.8 years ago by
Fátima Núñez
▴ 130
0
votes
6
replies
6.9k
views
DeSeq vs current version of Cuffdiff
Sequencing
Bayesian
Cancer
DESeq
Sequencing
Bayesian
Cancer
DESeq
updated 12.2 years ago by
Stephen Turner
▴ 290 • written 12.2 years ago by
Richard Friedman
★ 2.0k
0
votes
3
replies
6.7k
views
org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Cancer
Homo sapiens
convert
Cancer
Homo sapiens
convert
updated 15.2 years ago by
Seraya Maouche
▴ 10 • written 15.2 years ago by
Tim Smith
★ 1.1k
0
votes
2
replies
6.3k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP
Sequencing
Coverage
Alignment
Cancer
Biostrings
PROcess
IRanges
GenomicRanges
SNP
updated 10.5 years ago by
Michael Lawrence
★ 11k • written 10.5 years ago by
Hervé Pagès
16k
0
votes
3
replies
5.8k
views
multiple ColSideColors-type annotations on a heatmap
Cancer
annotate
Cancer
annotate
updated 15.0 years ago by
James F. Reid
▴ 610 • written 15.0 years ago by
Levi Waldron
★ 1.1k
0
votes
3
replies
5.7k
views
upregulated or downregulated?
Cancer
limma
Cancer
limma
updated 14.9 years ago by
Saroj K Mohapatra
▴ 400 • written 14.9 years ago by
biosciencegeek@gmail.com
▴ 20
0
votes
4
replies
5.6k
views
pca plot for gene expression
Cancer
Cancer
updated 9.8 years ago by
Michael Love
41k • written 9.8 years ago by
Guest User
★ 13k
1
vote
1
reply
5.4k
views
Limma: Contrasts comparing one factor to multiple others
Cancer
limma
Cancer
limma
updated 15.2 years ago by
James W. MacDonald
65k • written 15.2 years ago by
Daniel Brewer
★ 1.9k
2
votes
2
replies
4.8k
views
Genecards v3 access
Cancer
Cancer
updated 13.6 years ago by
Sean Davis
21k • written 13.6 years ago by
Daniel Brewer
★ 1.9k
0
votes
3
replies
4.8k
views
how to get gene list for given GO terms?
Pathways
GO
Cancer
PROcess
goTools
genomes
Pathways
GO
Cancer
PROcess
goTools
genomes
updated 22 months ago by
pengmin.wang.1
• 0 • written 12.2 years ago by
Marc Carlson
★ 7.2k
0
votes
2
replies
4.7k
views
gplots Heatmap
SNP
Transcription
Sequencing
RNASeq
miRNA
Microarray
Annotation
Normalization
GO
Cancer
updated 12.2 years ago by
Wolfgang Huber
★ 13k • written 12.2 years ago by
Polikepahad, Sumanth
▴ 10
0
votes
5
replies
4.6k
views
Finding mismatches between reads and reference sequence
Infrastructure
Cancer
BSgenome
BSgenome
Infrastructure
Cancer
BSgenome
BSgenome
updated 11.1 years ago by
David Greber
▴ 30 • written 11.1 years ago by
Hervé Pagès
16k
0
votes
0
replies
4.2k
views
Error in getClass(Class, where = topenv(parent.frame())) : "AnnotatedDataFrame" is not a defined class
Cancer
limma
Cancer
limma
15.3 years ago
Martin Morgan
25k
0
votes
16
replies
4.1k
views
subset a RleList using GRanges object?
Coverage
Cancer
IRanges
Coverage
Cancer
IRanges
updated 10.4 years ago by
Hervé Pagès
16k • written 10.4 years ago by
Janet Young
▴ 740
0
votes
0
replies
4.0k
views
[R] object is not subsettable
GO
Cancer
annotate
GO
Cancer
annotate
17.2 years ago
Seth Falcon
★ 7.4k
0
votes
4
replies
3.9k
views
supervised & unsupervised analysis of samples of microarray data
Cancer
Cancer
updated 12.0 years ago by
Steve Lianoglou
★ 13k • written 12.0 years ago by
wenhuo hu
▴ 200
0
votes
0
replies
3.8k
views
ComBat
Transcription
Genetics
Pathways
Network
Survival
Cancer
Breast
Colon
Kidney
Leukemia
HIV
11.5 years ago
SSc Array Core
▴ 10
1
vote
2
replies
3.8k
views
Partial NA coefficients for 10 probe(s) Limma
limma
microarray
cancer
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
everardoremi
• 0
0
votes
1
reply
3.7k
views
samtools error
Cancer
convert
Cancer
convert
updated 11.9 years ago by
Lucia Peixoto
▴ 330 • written 11.9 years ago by
Marcus Davy
▴ 390
1
vote
2
replies
3.7k
views
mixed model using limma-voom
limma
cancer
7.6 years ago
Yanzhu Lin
▴ 120
3
votes
0
replies
3.7k
views
biocLite() fails to install all limma dependencies from CRAN
Cancer
limma
Cancer
limma
17.0 years ago
Seth Falcon
★ 7.4k
0
votes
2
replies
3.6k
views
Web Scraping From Pubmd (I want to extract gene articles form pubmed abstract and pubmed id i want to extract for number of genes)
cancer
gene
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
venkatarao142152
• 0
0
votes
2
replies
3.6k
views
From location to get the SNP rs ID
SNP
Cancer
SNPlocs
ASSIGN
SNP
Cancer
SNPlocs
ASSIGN
updated 10.9 years ago by
Hervé Pagès
16k • written 10.9 years ago by
Fabrice Tourre
▴ 970
6
votes
2
replies
3.5k
views
Is ComBat introducing a signal where there is none?
Microarray
Clustering
Cancer
limma
Microarray
Clustering
Cancer
limma
10.4 years ago • updated 8.7 years ago
Vegard Nygaard
▴ 110
3
votes
2
replies
3.5k
views
Limma and logistic regression
Microarray
Cancer
limma
Microarray
Cancer
limma
updated 14.1 years ago by
Claus Mayer
▴ 340 • written 14.1 years ago by
Daniel Brewer
★ 1.9k
0
votes
2
replies
3.4k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer
tcga
normalization
rnaseq
differential gene expression
updated 6.1 years ago by
Dimitris Vavoulis
• 0 • written 9.0 years ago by
ezz
• 0
0
votes
14
replies
3.4k
views
Trimming of partial adaptor sequences
Sequencing
Cancer
Biostrings
Sequencing
Cancer
Biostrings
10.8 years ago
Taylor, Sean D
▴ 250
0
votes
0
replies
3.4k
views
Affymetrix HTA 2 array analysis
BiocViews
Annotation
Cancer
Breast
Organism
PROcess
biocViews
pdInfoBuilder
BiocViews
10.3 years ago
Elena Serrano
▴ 30
2
votes
5
replies
3.4k
views
Problem with BAM header in GAlignments
Cancer
Cancer
updated 10.3 years ago by
Martin Morgan
25k • written 10.3 years ago by
Taylor, Sean D
▴ 250
0
votes
1
reply
3.2k
views
a diffBind problem
Cancer
edgeR
DiffBind
Cancer
edgeR
DiffBind
11.2 years ago
Rory Stark
★ 5.1k
0
votes
5
replies
3.1k
views
overlap regions between two GRanges (or GRangesList)
Cancer
Cancer
updated 10.1 years ago by
Shanrong Zhao
▴ 20 • written 10.1 years ago by
Hervé Pagès
16k
0
votes
7
replies
3.1k
views
Visualise KEGG pathway and highlight genes
Cancer
KEGGgraph
Cancer
KEGGgraph
updated 15.0 years ago by
Paolo Sonego
▴ 140 • written 15.0 years ago by
Daniel Brewer
★ 1.9k
0
votes
14
replies
3.1k
views
pd.hugene.2.0.st missing normgene->exon mappings
Cancer
probe
Cancer
probe
updated 10.8 years ago by
James W. MacDonald
65k • written 10.8 years ago by
Mark Cowley
▴ 910
0
votes
3
replies
3.0k
views
Subsetting expression sets for mass spec data - second ask
Classification
Cancer
PROcess
Classification
Cancer
PROcess
updated 11.4 years ago by
Sean Davis
21k • written 11.4 years ago by
McGee, Monnie
▴ 300
0
votes
0
replies
3.0k
views
unique, duplicated, order, etc... on a GRanges object
Cancer
GenomicRanges
Cancer
GenomicRanges
12.7 years ago
Hervé Pagès
16k
0
votes
5
replies
3.0k
views
Finding genes with significant linear regression or trend
Microarray
Regression
Cancer
limma
DOSE
Microarray
Regression
Cancer
limma
DOSE
updated 15.9 years ago by
Ana Conesa
▴ 340 • written 15.9 years ago by
Daniel Brewer
★ 1.9k
0
votes
6
replies
3.0k
views
about ComBat plot for non parametric
Microarray
Cancer
Microarray
Cancer
updated 11.3 years ago by
hu duan
▴ 30 • written 11.3 years ago by
W. Evan Johnson
▴ 850
0
votes
6
replies
3.0k
views
Filtering before differential expression analysis of microarrays - New paper out
Cancer
Cancer
updated 15.3 years ago by
Gordon Smyth
50k • written 15.3 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
3.0k
views
DiffBind questions
Transcription
Cancer
DiffBind
MMDiff
Transcription
Cancer
DiffBind
MMDiff
10.7 years ago
Rory Stark
★ 5.1k
0
votes
11
replies
2.9k
views
Venn Diagram
Cancer
ABarray
Cancer
ABarray
updated 14.8 years ago by
SimonNoël
▴ 450 • written 14.8 years ago by
Hervé Pagès
16k
1
vote
1
reply
2.9k
views
DESeq2 plotPCA and scale
Cancer
Cancer
updated 9.8 years ago by
Michael Love
41k • written 9.8 years ago by
Daniel Brewer
▴ 100
0
votes
13
replies
2.9k
views
GEOmetadb and gse organism type
Cancer
Breast
Organism
GEOmetadb
Cancer
Breast
Organism
GEOmetadb
updated 15.1 years ago by
Sean Davis
21k • written 15.1 years ago by
Wacek Kusnierczyk
▴ 180
0
votes
10
replies
2.8k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer
RNAseqData
GenomicFeatures
Cancer
RNAseqData
GenomicFeatures
updated 9.8 years ago by
Fong Chun Chan
▴ 320 • written 9.8 years ago by
Valerie Obenchain
★ 6.8k
0
votes
1
reply
2.8k
views
CanceR: Survival plots
cancer
gui
survival
Kaplan-Meier
9.1 years ago • updated 9.0 years ago
kmezhoud
▴ 10
1
vote
1
reply
2.8k
views
Creat PWM from Alignment with Gaps
Alignment
Cancer
Alignment
Cancer
updated 10.5 years ago by
Lakshmanan Iyer
▴ 250 • written 10.6 years ago by
Hervé Pagès
16k
50 results • Page
1 of 1
Recent ...
Replies
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
by
Michael Love
41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
• 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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